‘Omics’ approaches for crop improvement

The growing human population and climate change are imposing unprecedented challenges on the global food supply [1]. To cope with these pressures, crop improvement demands enhancing important agronomical traits beyond yield, such as adaptation, resistance, and nutritional value, by pivoting direct and indirect selection approaches [2]. The development of next-generation high-throughput screening technologies, referred to as ‘omics’, promises to speed up plant trait improvement [3] while producing more sustainable crops. Large-scale techniques, such as genomics, transcriptomics, proteomics, metabolomics, and phenomics, have already provided large datasets for that purpose. Meanwhile, modern bioinformatic and machine-learning approaches are helping us to process this heterogeneous hyper-dimensional data [4] while ultimately understanding the mechanisms behind agronomic features within the contemporary plant breeding triangle (i.e., genomics vs. phenomics vs. enviromics) [5]. ‘Omics’ datasets are also being generated to study macro-scale interactions and deepen our knowledge of crop behavior across the microbial [6] and environmental [7,8] continua. However, despite these massive technological and computational developments [4], systemic efforts to integrate ‘omics’ studies to understand biochemical pathways and cellular networks of crop systems are in their infancy [9], especially in orphan species [10]. Therefore, this Special Issue envisions offering updated emergent views on large-scale ‘omics’-based approaches. Specifically, the compilation explores the conceptual framework of the ‘omics’ paradigm [11], the practical uses of multiple ‘omics’ technologies, and their integration through trans-disciplinary bioinformatics as tools to improve qualitative and quantitative traits in a diverse panel of crop species

Photosystem II Repair Cycle in Faba Bean May Play a Role in Its Resistance to Botrytis fabae Infection

Chocolate spot, which is caused by the necrotrophic fungus Botrytis fabae, is a major foliar disease occurring worldwide and dramatically reducing crop yields in faba bean (Vicia faba). Although chemical control of this disease is an option, it has serious economic and environmental drawbacks that make resistant cultivars a more sensible choice. The molecular mechanisms behind the defense against B. fabae are poorly understood. In this work, we studied the leave proteome in two faba bean genotypes that respond differently to B. fabae in order to expand the available knowledge on such mechanisms. For this purpose, we used two-dimensional gel electrophoresis (2DE) in combination with Matrix-Assisted Laser Desorption/Ionization (MALDI-TOF/TOF). Univariate statistical analysis of the gels revealed 194 differential protein spots, 102 of which were identified by mass spectrometry. Most of the spots belonged to proteins in the energy and primary metabolism, degradation, redox or response to stress functional groups. The MS results were validated with assays of protease activity in gels. Overall, they suggest that the two genotypes may respond to B. fabae with a different PSII protein repair cycle mechanism in the chloroplast. The differences in resistance to B. fabae may be the result of a metabolic imbalance in the susceptible genotype and of a more efficient chloroplast detoxification system in the resistant genotype at the early stages of infection

Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis

The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed

Responses and Differences in Tolerance to Water Shortage under Climatic Dryness Conditions in Seedlings from Quercus spp. and Andalusian Q. ilex Populations

Analyzing differences in tolerance to drought in Quercus spp., and the characterization of these responses at the species and individual population level, are imperative for the selection of resilient elite genotypes in reforestation programs. The main objective of this work was to evaluate differences in the response and tolerance to water shortage under in five Quercus spp. and five Andalusian Q. ilex populations at the inter- and intraspecies level. Six-month-old seedlings grown in perlite were subjected to drought treatments by withholding water for 28 days under mean 37 °C temperature, 28 W m-2 solar irradiance, and 41% humidity. The use of perlite as the substrate enabled the establishment of severe drought stress with reduction in water availability from 73% (field capacity) to 28% (dryness), corresponding to matric potentials of 0 and −30 kPa. Damage symptoms, mortality rate, leaf water content, photosynthetic, and biochemical parameters (amino acids, sugars, phenolics, and pigments) were determined. At the phenotypic level, based on damage symptoms and mortality, Q. ilex behaved as the most drought tolerant species. Drought caused a significant decrease in leaf fluorescence, photosynthesis rate, and stomatal conductance in all Quercus spp. analyzed, being less pronounced in Q. ilex. There were not differences between irrigated and non-irrigated Q. ilex seedlings in the content of sugar and photosynthetic pigments, while the total amino acid and phenolic content significantly increased under drought conditions. As a response to drought, living Q. ilex seedlings adjust stomata opening and gas exchange, and keep hydrated, photosynthetically active, and metabolically competent. At the population level, based on damage symptoms, mortality, and physiological parameters, the eastern Andalusian populations were more tolerant than the western ones. These observations inform the basis for the selection of resilient genotypes to be used in breeding and reforestation programs

A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species Quercus ilex

Holm oak (Quercus ilex) is the most important and representative species of the Mediterranean forest and of the Spanish agrosilvo-pastoral “dehesa” ecosystem. Despite its environmental and economic interest, Holm oak is an orphan species whose biology is very little known, especially at the molecular level. In order to increase the knowledge on the chemical composition and metabolism of this tree species, the employment of a holistic and multi-omics approach, in the Systems Biology direction would be necessary. However, for orphan and recalcitrant plant species, specific analytical and bioinformatics tools have to be developed in order to obtain adequate quality and data-density before to coping with the study of its biology. By using a plant sample consisting of a pool generated by mixing equal amounts of homogenized tissue from acorn embryo, leaves, and roots, protocols for transcriptome (NGS-Illumina), proteome (shotgun LC-MS/MS), and metabolome (GC-MS) studies have been optimized. These analyses resulted in the identification of around 62629 transcripts, 2380 protein species, and 62 metabolites. Data are compared with those reported for model plant species, whose genome has been sequenced and is well annotated, including Arabidopsis, japonica rice, poplar, and eucalyptus. RNA and protein sequencing favored each other, increasing the number and confidence of the proteins identified and correcting erroneous RNA sequences. The integration of the large amount of data reported using bioinformatics tools allows the Holm oak metabolic network to be partially reconstructed: from the 127 metabolic pathways reported in KEGG pathway database, 123 metabolic pathways can be visualized when using the described methodology. They included: carbohydrate and energy metabolism, amino acid metabolism, lipid metabolism, nucleotide metabolism, and biosynthesis of secondary metabolites. The TCA cycle was the pathway most represented with 5 out of 10 metabolites, 6 out of 8 protein enzymes, and 8 out of 8 enzyme transcripts. On the other hand, gaps, missed pathways, included metabolism of terpenoids and polyketides and lipid metabolism. The multi-omics resource generated in this work will set the basis for ongoing and future studies, bringing the Holm oak closer to model species, to obtain a better understanding of the molecular mechanisms underlying phenotypes of interest (productive, tolerant to environmental cues, nutraceutical value) and to select elite genotypes to be used in restoration and reforestation programs, especially in a future climate change scenario

Proteomic Changes in Paspalum fasciculatum Leaves Exposed to Cd Stress

Background: Cadmium is a toxic heavy metal that is widely distributed in water, soil, and air. It is present in agrochemicals, wastewater, battery waste, and volcanic eruptions. Thus, it can be absorbed by plants and enter the trophic chain. P. fasciculatum is a plant with phytoremediation capacity that can tolerate Cd stress, but changes in its proteome related to this tolerance have not yet been identified. (2) Methods: We conducted a quantitative analysis of the proteins present in P. fasciculatum leaves cultivated under greenhouse conditions in mining soils doped with 0 mg kg−1 (control), 30 mg kg−1, or 50 mg kg−1. This was carried out using the label-free shotgun proteomics technique. In this way, we determined the changes in the proteomes of the leaves of these plants, which allowed us to propose some tolerance mechanisms involved in the response to Cd stress. (3) Results: In total, 329 variable proteins were identified between treatments, which were classified into those associated with carbohydrate and energy metabolism; photosynthesis; structure, transport, and metabolism of proteins; antioxidant stress and defense; RNA and DNA processing; and signal transduction. (4) Conclusions: Based on changes in the differences in the leaf protein profiles between treatments, we hypothesize that some proteins associated with signal transduction (Ras-related protein RABA1e), HSPs (heat shock cognate 70 kDa protein 2), growth (actin-7), and cellular development (actin-1) are part of the tolerance response to Cd stress

Hereditary Leiomyomatosis and Renal Cell Cancer Syndrome in Spain: Clinical and Genetic Characterization

Simple Summary Hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome is a very rare hereditary disorder characterized by cutaneous leiomyomas (CLMs), uterine leiomyomas (ULMs), renal cysts (RCys) and renal cell cancer (RCC), with no data on its prevalence worldwide. No genotype-phenotype associations have been described. The aim of our study was to describe the genotypic and phenotypic features of the largest series of patients with HLRCC from Spain reported to date. Of 27 FH germline pathogenic variants, 12 were not previously reported in databases. Patients with missense pathogenic variants showed higher frequencies of CLMs, ULMs and RCys, than those with loss-of-function variants. The frequency of RCCs (10.9%) was lower than those reported in the previously published series. Hereditary leiomyomatosis and renal cell cancer syndrome (HLRCC) is a very rare hereditary disorder characterized by cutaneous leiomyomas (CLMs), uterine leiomyomas (ULMs), renal cysts (RCys) and renal cell cancers (RCCs). We aimed to describe the genetics, clinical features and potential genotype-phenotype associations in the largest cohort of fumarate hydratase enzyme mutation carriers known from Spain using a multicentre, retrospective study of individuals with a genetic or clinical diagnosis of HLRCC. We collected clinical information from medical records, analysed genetic variants and looked for genotype-phenotype associations. Analyses were performed using R 3.6.0. software. We included 197 individuals: 74 index cases and 123 relatives. CLMs were diagnosed in 65% of patients, ULMs in 90% of women, RCys in 37% and RCC in 10.9%. Twenty-seven different pathogenic variants were detected, 12 (44%) of them not reported previously. Patients with missense pathogenic variants showed higher frequencies of CLMs, ULMs and RCys, than those with loss-of-function variants (p = 0.0380, p = 0.0015 and p = 0.024, respectively). This is the first report of patients with HLRCC from Spain. The frequency of RCCs was lower than those reported in the previously published series. Individuals with missense pathogenic variants had higher frequencies of CLMs, ULMs and RCys

Bioquímica y proteómica vegetal y agrícola

En la presente comunicación se resume lo que ha sido la actividad investigadora del grupo “Bioquímica y Proteómica Vegetal y Agrícola” (PAI AGR-164) en los últimos tres años (2005-2007). Nuestro interés y objetivo científico se ha centrando en el estudio de los cambios adaptativos y reacciones de defensa y de resistencia/tolerancia de las plantas a estreses de tipo biótico (hongos fitopatógenos y plantas parásitas) y abiótico (metales pesados, sequía). Dichos estudios se han llevado a cabo tanto con sistemas modelo (Arabidopsis thaliana y Medicago truncatula), como con especies de interés agronómico (garbanzo, girasol, guisante, maíz) o forestal (encina, alcornoque y pino). En los proyectos de investigación abordados se ha utilizado, en gran medida, una aproximación de proteómica, y también técnicas de bioquímica clásica y transcriptómica. La proteómica constituye, hoy en día, una línea prioritaria en cualquier investigación biológica, suministrando, en el área de la biología vegetal, y en combinación con las técnicas clásicas de bioquímica y las de transcriptómica, información relevante sobre diferentes aspectos básicos y aplicados relacionados con especies de interés agronómico y forestal, como es el de la respuesta a estreses, y la caracterización de genotipos (poblaciones, mutantes, líneas transgénicas). Además, hay aspectos, como el de las modificaciones postraduccionales, que sólo pueden ser abordados experimentalmente mediante una estrategia de proteómica. Nuestro grupo ha iniciado recientemente una nueva línea, dirigida a estudiar el proteoma redox en Arabidopsis y su implicación en la respuesta a patógeno

Risk of cancer in family members of patients with lynch-like syndrome

Lynch syndrome (LS) is a common cause of hereditary colorectal cancer (CRC). Some CRC patients develop mismatch repair deficiency without germline pathogenic mutation, known as Lynch-like syndrome (LLS). We compared the risk of CRC in first-degree relatives (FDRs) in LLS and LS patients. LLS was diagnosed when tumors showed immunohistochemical loss of MSH2, MSH6, and PMS2; or loss of MLH1 with BRAF wild type; and/or no MLH1 methylation and absence of pathogenic mutation in these genes. CRC and other LS-related neoplasms were followed in patients diagnosed with LS and LLS and among their FDRs. Standardized incidence ratios (SIRs) were calculated for CRC and other neoplasms associated with LS among FDRs of LS and LLS patients. In total, 205 LS (1205 FDRs) and 131 LLS families (698 FDRs) had complete pedigrees. FDRs of patients with LLS had a high incidence of CRC (SIR, 2.08; 95% confidence interval (CI), 1.56-2.71), which was significantly lower than that in FDRs of patients with LS (SIR, 4.25; 95% CI, 3.67-4.90; p < 0.001). The risk of developing other neoplasms associated with LS also increased among FDR of LLS patients (SIR, 2.04; 95% CI, 1.44-2.80) but was lower than that among FDR of patients with LS (SIR, 5.01, 95% CI, 4.26-5.84; p < 0.001). FDRs with LLS have an increased risk of developing CRC as well as LS-related neoplasms, although this risk is lower than that of families with LS. Thus, their management should take into account this increased risk

Desarrollo de herramientas metodológicas para incorporar contenidos de ciencia al aula y su valoración económica

La ciencia y la tecnología juegan un papel fundamental en nuestra sociedad. En este sentido, la ciudadanía parece necesitar unos conocimientos básicos que le permitan responder de manera autónoma a multitud de situaciones, tanto a nivel personal como social (Kolstø et al., 2006). Este requisito, conocido en la literatura como alfabetización científica, lleva siendo uno de los objetivos de la educación en las últimas décadas (Hodson, 2003; Feinstein, 2011). Sin embargo, parece que su consecución presenta algunos problemas. Una de las causas de estas dificultades parece ser la falta de conexión entre los contenidos que se trabajan en las clases y el día a día del ciudadano. Respecto a esto, una solución ampliamente citada en la literatura es contextualizar el aprendizaje, relacionando los contenidos trabajados en clase con escenarios cotidianos y familiares para el alumnado (Clegg & Kolodner, 2014). El proyecto pretendía que nuestros estudiantes llevasen a cabo un análisis de los contextos con contenidos científico-económicos y promovieran su utilización en el aula y en su futuro profesional. Es decir, formar a nuestros profesionales para que pudieran detectar e incorporar entre sus competencias la capacidad de conectar lo aprendido en las asignaturas con las necesidades sociales. En concreto, el proyecto tenía, en base a los problemas detectados en la percepción de la ciencia y en la formación de los ciudadanos, dos grandes tipos de objetivos: Objetivos relacionados con la percepción de los conocimientos científico-tecnológicos y su valoración económica (Ezquerra, Fernández-Sánchez, Cabezas, 2013; Ezquerra, Fernandez-Sanchez, 2014; Ezquerra, Fernandez-Sanchez, Magaña, 2015; 2016; Ezquerra, Fernandez-Sanchez, Magaña & Mingo, 2017): • Identificar en qué situaciones los ciudadanos, en su vida cotidiana, están en presencia de contenidos científicos o tecnológicos. • Determinar de qué modo llegan al ciudadano estos contenidos, con qué intensidad, cómo son propuestos, cómo son percibidos... • Analizar el modo en que podemos otorgar a estos contenidos una valoración económica. Objetivos educativos que se integran dentro de las asignaturas: • Analizar las correspondencias entre los currículos oficiales y los contenidos presentes en el entorno del ciudadano (Ezquerra, Fernandez-Sanchez, Magaña Ramos, 2015; Ezquerra y Magaña, 2016). • Introducir a los estudiantes en una propuesta de aprendizaje basada en la indagación (Rivero et al., 2013; Ezquerra, De Juanas, Martín del Pozo, 2015). • Valorar las estrategias y competencias de los futuros docentes para vincular sus conocimientos con la realidad circundante (De Juanas et al., 2012). • Analizar las actividades que los estudiantes propongan para identificar los contenidos de ciencia y estudiar su valoración económica